Removing .venv results in …
[galaxy@storage1 ~]$ sh run.sh
Found conda at: /home/.galaxy/database/dependencies/_conda/bin/conda
Found Conda, virtualenv will not be used.
To use a virtualenv instead, create one with a non-Conda Python 2.7 at .venv
Activating Conda environment: _galaxy_18.09
And it then tries to establish a non-venv/conda installation which fails because of the certifi clash.
The installation readme says to run the run.sh after the git pull to finalise the upgrade - so I dont see how starting the Galaxy installation from supervisord is involved in the maintenance of deps.
The .venv version of the installation will not install yarn due to a similar issue with packages not agreeing on how they should be uninstalled. Seems to only happen on systems where the package scertifi and already exist and requires removal and reinstallation, or yarn must be installed by npm into a pre-existing .venv …
Anyhow thanks for thinking about all this - hope we are not boring you